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Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

Yuan O. Zhu, Gavin Sherlock, Dmitri A. Petrov
doi: https://doi.org/10.1101/044958
Yuan O. Zhu
*Departments of Genetics.
†Biology Stanford University, Stanford, CA 94305.
‡Genome Institute of Singapore, Singapore 138672.
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Gavin Sherlock
*Departments of Genetics.
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Dmitri A. Petrov
†Biology Stanford University, Stanford, CA 94305.
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ABSTRACT

Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 145 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeasts genomes, with 35 strains showing partial chromosomal copy number changes and 8 strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2x increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information of the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in yeast adaptation.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 21, 2016.
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Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation
Yuan O. Zhu, Gavin Sherlock, Dmitri A. Petrov
bioRxiv 044958; doi: https://doi.org/10.1101/044958
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Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation
Yuan O. Zhu, Gavin Sherlock, Dmitri A. Petrov
bioRxiv 044958; doi: https://doi.org/10.1101/044958

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